US6790616B1 - Method for typing of HLA class I alleles - Google Patents

Method for typing of HLA class I alleles Download PDF

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US6790616B1
US6790616B1 US09/856,662 US85666201A US6790616B1 US 6790616 B1 US6790616 B1 US 6790616B1 US 85666201 A US85666201 A US 85666201A US 6790616 B1 US6790616 B1 US 6790616B1
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hla
alleles
allele
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Toyoki Moribe
Toshihiko Kaneshige
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Shionogi and Co Ltd
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/113—PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • HLA Human Leukocyte Antigen
  • HLA Human Leukocyte Antigen
  • the present invention relates to a method, a reagent and a kit for typing of the HLA class I alleles.
  • This invention is especially useful for judgement of compatibility between a donor and a recipient in organ transplantation, and for association analysis between the HLA class I genes and various types of diseases in the clinical and medical field. This invention enables us to easily automate and mechanize detection and determination of the HLA class I alleles.
  • HLA antigens have been mainly performed by the serological method using human alloantibodies.
  • complement-mediated cytotoxicity is caused in the antigen-antibody reaction. It changes permeability of positive cell membranes to take an eosinic pigment into the cell, resulting in being detected as colored and expanding cells with a microscope.
  • HLA-A, HLA-B and HLA-C antigens belonging to HLA class I, and HLA-DR and HLA-DQ antigens belonging to HLA class II by this method.
  • this method has problems in terms of collection, quality control and supply of the specific antibodies.
  • the survival rate of cells is utilized as an indicator for judgement in this method. Therefore, poor conditions of subjects, for example, a low survival rate of cells caused by disease or influence by passage of time after blood collection, lead to decrease of credibility for results of testing.
  • PCR-SSOP Sequence-Specific Oligonucleotide Probe
  • PCR-RFLP Restriction Fragment Length Polymorphism
  • PCR-SSP Sequence-Specific Primers
  • PCR-SSCP Single Strand Conformation Polymorphism
  • HLA class I genes including non-classical genes (HLA-E, -F and -G) and pseudogenes (HLA-H, -J, -K and -L), are highly homologous among them.
  • HLA class I DNA typing methods have been reported. However, all these methods require complicated manipulation, strict reaction condition and skill. Those are not suitable for handling a large number of samples and offer only low resolution HLA typing. Furthermore, the typing methods for each gene are not standardized.
  • the purpose of this invention is to solve problems of the manipulation of HLA class I locus antigen typing by the classical serological method, and to prodive a method, a kit and a reagent for classifing the subtype of the HLA class I antigens at the allele level (allele typing), which has not been distinguished by the classical method. Furthermore, the aim of this invention is to provide a method for typing of the HLA class I alleles which can automate and machanize easily.
  • the inventors have established primers which can amplify all the HLA-A alleles, all the HLA-B alleles or all the HLA-C alleles and specific primers to the common sequences among all alleles in the group consisting of the specific HLA-A alleles or the specific HLA-B alleles.
  • the inventors have established probes which can specifically hybridize with the sequence of at least one specific HLA-A allele, at least one specific BLA-B allele or at least one specific HLA-C allele.
  • the inventors have found out that it is possible to distinguish the HLA class I antigen or allele, by hybridizing the PCR amplified products derived from the specific HLA class I allele or the specific group with the DNA probes described above which are immobilized on wells of microtiter plates, adding an enzyme-conjugate which can specifically bond to a label of the amplified products at the same time as or after the hybridization, and adding a chromogenic substrate, a luminescent substrate or a fluorescent substrate to the mixture, to detect as signals whether or not the amplified products are hybridized with the immobilized DNA probes.
  • an enzyme-conjugate which can specifically bond to a label of the amplified products at the same time as or after the hybridization
  • adding a chromogenic substrate, a luminescent substrate or a fluorescent substrate to the mixture, to detect as signals whether or not the amplified products are hybridized with the immobilized DNA probes.
  • the main embodiment of this invention is a method for typing of HLA class I alleles, which comprises the following steps from (a) to (d).
  • the PCR amplification of the target gene at the step (a), can be classified into 2 steps.
  • the other is a step to selectively amplify the specific group consisting of the specific HLA-A allele group or the specific HLA-B allele group by the PCR method using a primer pair which is specific to the common sequences to alleles of the specific group consisting of the specific HLA-A alleles or the specific HLA-B alleles.
  • PCR primers are designed to be specific to the common sequences, which are within the region of all alleles belonging to the HLA-A allele, the HLA-B allele or the HLA-C allele, or ahead and behind the region.
  • PCR primers are designed to be specific to the common sequences to all all alleles included in the specific group in order to amplify the specific group.
  • the primers described above don't need to be used for both a sense primer and an anti sense primer of a primer pair corresponding to the specific group. It is possible to use the specific primer to the specific group for one of primers and the specific primer to all the groups for the other. The latter step can be performed according to the reference described by the inventors (Tissue Antigens 1997, Vol.50, 535-545). A method to selectively amplify alleles encoding the HLA-A2 antigen or the HLA-B40 antigen as a group is disclosed in the present description.
  • the PCR-amplified products derived from the allele belonging to the HLA-A alleles, the HLA-B alleles or the HLA-C alleles, or from the specific group, are produced. But it is not possible to distinguish the type of the HLA class I allele at the step.
  • the hybridization reaction at the step (b) using the specific DNA probes is applied to the following steps.
  • the Typing Table at the step (d) is made using signal patterns obtained by hybridizing the PCR amplified products from samples whose HLA class I antigen types or allele types are known, with DNA probes which can specifically hybridize with the sequence of at least one specific HLA class I allele.
  • Persons skilled in the art can make easily the Typing Table.
  • FIGS. 1 to 6 can be referred. If someone wants to use DNA probes, which are not described in this description, another Typing Table can be used.
  • the Typing Table is made from signal patterns obtained by hybridizing the PCR amplified products from samples whose HLA class I antigen types or allele types are known, with another DNA probe. As described above, persons skilled in the art can also make easily these Typing Tables. It should be considered that each sample has the HLA class I allele type in a homozygous or heterozygous state, when the HLA class I allele type is distinguished according to the Typing Tables.
  • the PCR method at the step (a) is performed by using a primer pair in which at least one of them is labeled, in order to detect whether or not the amplified products hybridize with immobilized DNA probes as signals at the step (c) described above.
  • the above PCR can be performed by using 4 kinds of deoxyribonucleotide triphosphate (dNTP) in which at least one of them is labeled.
  • dNTP deoxyribonucleotide triphosphate
  • a radioisotopic substance, or a non-radioisotopic substance such as a biotin or a digoxigenin, can be utilized.
  • the hybridization of the products amplified by the PCR method with the immobilized DNA probe is performed by addiing an enzyme-conjugate which can specifically bond to a label of the amplified products is added at the same time as hybridization or after, and the amplified products hybridizing with the immobilized DNA probe is detected as signals by adding a chromogenic substrate, a luminescent substrate or a fluorescent substrate which can specifically react with the enzyme.
  • an enzyme-conjugated streptavidin is used as an enzyme-conjugate, the signal can be immediately detected after washing by adding an enzyme-conjugate at the same time as hybridization.
  • At least one of a primer pair at the step (a) described above is biotinylated, and an enzyme-conjugate which can specifically bond to the biotinylated label at the step (b) or (c) is an enzyme-conjugated streptavidin, for example, a peroxydase-conjugated streptavidin or an alkaline phosphatase-conjugated streptavidin.
  • the hybridization of the products amplified by the PCR method with immobilized DNA probes is performed in a solution containing formamide at the step (b) described above.
  • the formamide concentration of the solution described above is from 5% to 30%, and from 10% to 25% as a preferable concentration.
  • the concentration can be changed according to the sequence, the length and the type of the used DNA probe.
  • the most preferable formamide concentration is about 20%.
  • the hybridization at the step (b) is performed in a solution containing formamide at the temperature of the 37° C.
  • the preferable temperature is from 32° C. to 42° C.
  • the temperature can be changed according to the sequence, the length and the type of the used DNA probe as mentioned above for the formamide concentration.
  • the most desirable temperature is about 37° C.
  • Hybridization is usually performed at comparatively high temperature, at about 65° C., to improve the specificity.
  • the reaction can be performed at low temperature, at about 37° C.
  • the temperature for washing after hybridization of the amplified products by the PCR method with immobilized DNA probes and/or after binding a label of the amplified products with an enzyme-conjugate is performed at room temperature. Namely, washing can be performed at low temperaure like room temperature as by using the solution containing formamide, as well as the above hybridization.
  • the amino-modified DNA which can specifically hybridize with at least one specific HLA-A allele, used at the step (b) in this invention can be selected from the group consisting of A98T (SEQ ID No.:1), A98A (SEQ ID No.:2), A160A (SEQ ID No.:3), A239A (SEQ ID No.:4), A238A (SEQ ID No.:5), A240T (SEQ ID No.:6), A257TC (SEQ ID No.:7), A259AC (SEQ ID No.:8), A270T (SEQ ID No.:9), A282C (SEQ ID No.:10), A290T (SEQ ID No.:11), A299T (SEQ ID No.:12), A302G (SEQ ID No.:13), A355G (SEQ ID No.:14), A362TA (SEQ ID No.:15), A362TT (SEQ ID No.:16), A368A (SEQ ID No.
  • the amino-modified DNA probe which can specifically hybridize with at 10 least one specific HLA-B allele can be selected from the group consisting of BL1 (SEQ ID No.:36), BL3 (SEQ ID No.:37), BL4 (SEQ ID No.:38), BL5 (SEQ ID No.:39), BL9 (SEQ ID No.:40), BL10 (SEQ ID No.:41), BL11 (SEQ ID No.:42), BL24 (SEQ ID No.:43), BL25 (SEQ ID No.:44), BL34 (SEQ ID No.:45), BL35 (SEQ ID No.:46), BL36 (SEQ ID No.:47), BL37 (SEQ ID No.:48), BL38 (SEQ ID No.:49), BL39 (SEQ ID No.:50), BL40 (SEQ ID No.:51), BL41 (SEQ ID No.:52), BL42 (SEQ ID No.:53), BL56 (S
  • the amino-modified DNA probe which can specifically hybridize with at least one specific HLA-C allele can be selected from the group consisting of CC (SEQ ID No.:68), A-12 (SEQ ID No.:69), A-2 (SEQ ID No.:70), A-3 (SEQ ID No.:71), A-4 (SEQ ID No.:72), A-54 (SEQ ID No.:73), B-1 (SEQ ID No.:74), B-2 (SEQ ID No.:75), C-12 (SEQ ID No.:76), C-24 (SEQ ID No.:77), C-33 (SEQ ID No.:78), C-43 (SEQ ID No.:79), 134-g (SEQ ID No.:80), 134-A2 (SEQ ID No.:81), 353TCA1 (SEQ ID No.:82), 343A (SEQ ID No.:83), RA-2 (SEQ ID No.:116), RA-41 (SEQ ID No.:117), RB-28 (SEQ ID No
  • This invention also comprises the DNA probe itself (from SEQ ID No.: 1 to SEQ ID No.:83 and from SEQ ID No.:100 to SEQ ID No.:130) which can specifically hybridize with at least one specific HLA-A allele, at least one specific HLA-B allele or at least one specific HLA-C allele for using the method for distinguishing the HLA class I allele type.
  • Both an amino-modified DNA probe and an unmodified DNA probe can be used.
  • the amino-modified probe must be used.
  • Some bases can be deleted from or added to the end of the DNA probe within the range that the DNA probe can specifically hybridize with at least one specific HLA-A allele, at least one specific HLA-B allele or at least one specific HLA-C allele, namely, within the range that the DNA probe can keep the original specificity of hybridization.
  • the DNA probes in this invention also comprise DNA probes wtherein some bases are deleted from or added to the nucleic acid sequence from SEQ ID No.:1 to SEQ ID No.:83 and SEQ ID No.:100 to SEQ ID No.:130 within the range described above.
  • the primers which can amplify all the HLA-A alleles, all the HLA-B alleles or all the HLA-C alleles at the step (a) in this invention can be selected from the group consisting of CGA011 (SEQ ID No.:90), CGA012 (SEQ ID No.:91), AIn3-66C (SEQ ID No.:92), 5BCIn37-34C (SEQ ID No.:96), 5BCIn37-24g (SEQ ID No.:97) and 5BCIn37-34g2 (SEQ ID No.:99).
  • the primer which is specific to the common sequence to alleles of the specific group consisting of the specific HLA-A alleles or the specific HLA-B alleles can be selected from A2-5T (SEQ ID No.:84), A3-273T (SEQ ID No.:85), A4-8C (SEQ ID No.:86), A4-254G (SEQ ID No.:87), BASF-1 (SEQ ID No.:88), and BASR-1 (SEQ ID No.:89).
  • This invention comprises the primer itself described above (from SEQ ID No.:88 to SEQ ID No.:92, from SEQ ID No.:96 to SEQ ID No.:97 and SEQ ID No.:99), used for the method to type the HLA class I alleles.
  • Novel HLA-A alleles, HLA-B alleles and HLA-C alleles have been discovered.
  • WHO World Health Organization
  • Nomenclature Committee for the HLA system 82, 186, and 42 of alleles have been assigned for the HLA-A, -B and -C loci, respectively, at March 1997.
  • This invention can discriminate all these alleles.
  • the method shown in this invention, together with an optional, easy-performed improvement, such as adding extra DNA probes or primers, can cope with discrimination of alleles which may be discovered and enrolled in the future.
  • kits and a reagent for typing of the HLA class I alleles described in this description.
  • this invention can provide a kit and a reagent which comprise the DNA probes and the primers described in this description.
  • the kit can comprises a solution containing the primers (from SEQ ID No.:84 to SEQ ID No.:92, from SEQ ID No.:96 to SEQ ID No.:97 and SEQ ID No.:99) which is disclosed in this invention, PCR buffer solution, which may be concentrated solution, dNTPs, thermostable DNA polymerase, the DNA probes (from SEQ ID No.:84 to SEQ ID No.:92, from SEQ ID No.:96 to SEQ ID No.:97 and SEQ ID No.:99) which is disclosed in this invention or a microtiter plate on whose wells the DNA probes are covalently immobilized, a denature solution, a hybridization buffer, a washing solution and an instruction for the kit which includes the Typing Table
  • the primer described above can optionally be labeled with a radioisotopic or non-radioisotopic substance.
  • the primers can form a primer pair.
  • the solution containing the primer can be freeze-dried.
  • at least one of four kinds of dNTPs must be labeled.
  • an enzyme-conjugate solution, a chromogenic reagent including a chromogenic substrate and a chromogenic solution, a luminescent reagent or a fluorescent reagent, a stop solution and so on can be added as a component in the kit.
  • a component such as guanidine thiocyanate buffer for isolation of genome DNAs, can be optionally added in the kit to the degree promoting enforcement of this invention.
  • FIG. 1 indicates a Typing Table showing the reaction pattern between samples which the HLA-A2 allele type is known and DNA probes in the present invention. Each name of DNA probes is shown on the top in the Figure, and each type of the HLA-A2 alleles is shown on the left side in the Figure. Closed square and Open square mean a positive and a negative reaction, respectively.
  • FIG. 2 indicates a Typing Table showing the reaction pattern between samples which the HLA-B40 allele type is known and DNA probes in the present invention. Each name of DNA probes is shown on the top in the Figure, and each type of the HLA-B40 alleles is shown on the left side in the Figure. Closed square and Open square mean a positive and a negative reaction, respectively.
  • FIG. 3 indicates a Typing Table showing the reaction pattern between samples which the HLA-A antigen and allele type are known, and DNA probes in the present invention. Each name of DNA probes is shown on the top in the Figure, and each type of the HLA-A antigens and alleles is shown on the left side in the Figure. Closed square and Open square mean a positive and a negative reaction, respectively.
  • FIGS. 4 and 5 indicate Typing Tables showing the reaction pattern between samples which the HLA-B antigen and allele type is known, and DNA probes in the present invention. Each name of DNA probes is shown on the top in the Figures, and each type of the HLA-B antigens and alleles is shown on the left side in the Figures. Closed square and Open square mean a positive and a negative reaction, respectively.
  • FIG. 6 indicates a Typing Table showing the reaction pattern between samples which the HLA-C antigen and/or allele type is known, and DNA probes in the present invention. Each name of DNA probes is shown on the top in Figure, and each type of the HLA-C and/or alleles is shown on the left side in Figure. Closed square and Open square mean a positive and a negative reaction, respectively.
  • the typing method in this invention can be explained, dividing into the following 6 steps.
  • a method for preparation of genome DNAs is explained as follows. Leukocytes are isolated from collected blood according to usual methods and are lysed in a guanidine thiocyanate buffer. Proteins are eliminated by phenol extraction. A sodium acetate buffer (pH 5.2) is added and mixed. Genome DNAs are obtained by adding chilled ethanol.
  • the region containing the HLA class I allele is amplified by the PCR method using genome DNAs described above for a template.
  • Commercialized reagents can be used for amplification described above. Amplification can be performed according to attached instructions. If it is necessary, reaction temperature, reaction time, the number of cycles and so on can be changed. Then, the amplification is performed by using a primer pair for a reaction tube. Amplification by adding multiple primer pairs into the same reaction tubes, can decrease operation task or cost. From the viewpoint of the purpose of this invention, a primer pair which one of them is biotinylated, is used for the practical testing or a kit.
  • A2-5T and 5′-biotinylated A3-273T can be used for a primer pair to amplify the region containing the exon 2, the intron 2 and the exon 3 of the HLA-A2 alleles by the PCR method.
  • A4-8C and 5′-biotinylated A4-254G can be used for a primer pair to amplify the region containing the exon 4 of the HLA-A alleles by the PCR method.
  • BASF-1 and 5′-bitinylated BASR-1 can be used for a primer pair to amplify the region containing the exon 2, the intron 2 and the exon 3 of the HLA-B40 alleles by the PCR method.
  • CGA011 or CGA012 and 5′-biotinylated AIn3-66C can be used for a primer pair to amplify the region containing the exon 2, the intron 2 and the exon 3 of all the HLA-A alleles by the PCR method.
  • 5BIN1-TA SEQ ID No.:93
  • 5BIN1-CG SEQ ID No.:94
  • 5′-biotinylated 3BIN3-37 SEQ ID No.:95
  • the primers are described in the reference of Cereb N. et al (Tissue Antigens 1997, Vol.50, 74-76)
  • 5BCIn37-34C, 5BCIn37-24g or 5BCIn37-34g2, and 5′-biotinylated 3BCIn3-12 can be used for a primer pair to amplify the region containing the exon 2, the intron 2 and the exon 3 of all the HLA-C alleles by the PCR method.
  • the primer, 3BCIn3-12 is described in the reference of Cereb N. et al (Tissue Antigens 1995, Vol.45, 1-11).
  • Amino-modified DNA probes (1-20 pmol) which can specifically hybridize with the sequence of at least one specific HLA-A allele, at least one specific HLA-B allele or at least one specific HLA-C allele, are added onto each well of carboxylate-modified polystyrene microtiter plates and immobilized covalently by inducing the chemical amino-binding reaction using a suitable catalyst, for example, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). After immobilization of the DNA probes on wells, microtiter plates are washed with a suitable buffer. After washing, microtiter plates can be stored over an extended period of time on wet and cold condition.
  • a suitable catalyst for example, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC).
  • the PCR amplified products are denatured to a single strand DNA under strong alkali, for example, NaOH, and are hybridized with DNA probes which are immobilized on wells of microtiter plates.
  • the hybridization is performed in a solution containing about 20% formamide on hybridization condition at about 37° C. After the hybridization, excessive amplified products or those which don't have the specific sequence to DNA probes described above, are eliminated.
  • DNA probes used at this step are selected in compliance with the specific HLA class I gene or the specific group which are amplified at the above step.
  • the hybridization can be performed by using A98T, A98A, A160A, A240T, A270T, A290T, A355G, A362TA, A362TT, A368A, A368G, A368T, A402G, A485A, A527A, A539A, A539T A559G, A570CG, A779A or A843A for DNA probes.
  • the hybridization can be performed by using BL4, BL5, BL24, BL25, BL34, BL35, BL37, BL39, BL41, BL50, BL56, BL57, BL222A, BL409T or BL512 for DNA probes.
  • the hybridization can be performed by using A34, A239A, A238A, A257TC, A259AC, A282C, A282CT, A290TR, A299T, A355G, A414A, A448C, A468T, A489A, A502C, A526T, A538CG, A538TG, A539A, A539T, A555T, A570CG, A570GT or A302GR for DNA probes.
  • the hybridization can be performed by using BL1, BL3, BL4, BL9, BL10, BL11, BL34, BL36, BL37, BL38, BL39R, BL40, BL41, BL42, BL77, BL78, BL79, BL226G, BL263T, BL272A, BL527A, BL538CG, BL538G or BL570GT for DNA probes.
  • the hybridization can be performed by using 201g1, C206gR, A-12, RA-2, A-3, RA-41, A-54, B-1, RB-28, C-12, C-24, C-33, C-43, 134-g, 134-A2, 353TCA1, 343A, R341A, R343g3, 353TCC, 361T1, 361T368g, 361T368T1, 369C, 387g1, 526AC2 or 538gAC for DNA probes.
  • A302G, A423T, A524G, BL272GA, BL292G, BL292T, BL361G, CC, A-2, A-4 or B-2 can be used for typing of the HLA class I antigens or alleles described below.
  • A302G, A423T and A524G can specifically hybridize with the sequence of the HLA-A antigens or alleles, A*2501 and A*3201, A*2501, A26, A34, A*4301 and A66, and A*2301, A29, A*31012, A*3201, A33 and A*7401, respectively.
  • BL272GA, BL292G, BL292T and BL361G can specifically hybridize with the sequence of the HLA-B antigens or alleles, B14, B38 and B39, B7, B8, B14, B27, B39, B*4201, B*4601, B*5401, B55, B56, B67, B*7301, B*7801 and B*8101, B13, B15, B18, B35, B37, B38, B40, B41, B44, B*4501, B*4701, B48, B*4901, B*5001, B51, B52, B5301, B57, B58, B*5901 and B*7802, and B57, respectively.
  • CC can hybridize with the sequence of all the HLA-C alleles.
  • A-2, A-4 and B-2 can specifically hybridize with the sequence of the HLA-C antigens or alleles, Cw2, Cw3, Cw*0403 and Cw15, Cw*0602, Cw7 and Cw18, and Cw1, Cw3, Cw7, Cw8, Cw*1202, Cw*1203, Cw*1301, Cw14, Cw*1601 and Cw*16041, respectively.
  • the PCR amplified products hybridizing with DNA probes can be detected by utilizing a label, which they have in themselves, such as a biotin. After an alkaline phosphate-conjugated streptavidin or a peroxidase-conjugated streptavidin which can bond to a biotin, is added to each well of the microtiter plates, and the plates are sealed, the reaction is performed by incubation on proper temperature condition.
  • the hybridizing amplified products are detected as signals by using a chromogenic substrate such as p-nitrophenylphosphate (PNPP) or 3,3′,5,5′-tetramethylbenzidine (TMB). Detection of signals is performed by measurement of the absorbance.
  • PNPP p-nitrophenylphosphate
  • TMB 3,3′,5,5′-tetramethylbenzidine
  • Leukocytes (Samples 1-4) which were isolated from peripheral blood (about 10 ml) of normal subjects according to usual methods, were lysed in 500 ⁇ l of guanidine thiocyanate buffer (4M guanidine thiocyanate, 25 mM sodium citrate(pH7.0), 0.5% sodium N-lauroylsarcosinate, 1% mercaptoethanol). The solution was extracted twice with phenol to eliminate proteins. After mixing with 3M sodium acetate buffer (pH 5.2), genome DNAs were obtained by adding twice volume of chilled ethanol. By using this DNAs, typing of the HLA-A2 alleles was performed as follows.
  • the reaction solution was composed of genomic DNAs (100 ng), 1.4 units of thermostable DNA polymerase which was pretreated with Taq StartTMAntibody for 5 min at room temperature, 67 mM Tris-HCl (pH 8.8), 16.6 mM ammonium sulfate, 1.5 mM magnesium chloride, 0.01% Tween 20, 200 ⁇ M dNTPs, and each 1.7 ⁇ M of a primer pair in a final volume of 80 ⁇ l.
  • DNA amplification was performed by using GeneAmp PCR system 9600 (Perkin Elmer) by initial denaturation at 95° C. for 2 min followed by 5 cycles of denaturation for 25 s, annealing at 70° C. for 45 s, extension at 72° C. for 45 s followed by 36 cycles of denaturation for 25 s, annealing at 65° C. for 50 s, extension at 72° C. for 45 s.
  • 5′-amino-modified DNA probes A98T, A98A, A160A, A240T, A270T, A290T, A355G, A362TA, A362TT, A368A, A368G, A368T, A402G, A485A, A527A, A539A, A539T A559G, A570CG, A779A and A843A, were immobilized covalently on wells of carboxylate-modified polystyrene microtiter plates as follows. Twenty-five ⁇ l of the DNA probes described above which were dissolved with sterile distilled water, was added to each of 20 wells which were used for a sample, in order shown in FIG. 1 .
  • EDC 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
  • GMC buffer for hybridization (0.25M di-sodium hydrogenphosphate, 7% SDS, 1% BSA, 0.5M EDTA, 0.03M phosphoric acid, 20% formamide) was added to each well of the microtiter plates and the plates were incubated for 5 min at 37° C. After incubation, the buffer was removed from each well. During incubation, 72 ⁇ l of the amplified products which were obtained from the region containing the exon 2, the intron 2 and the exon 3, and 8 ⁇ l of the amplified products which were obtained from the region containing the exon 4, were denatured with an equivalent volume of 0.4 NaOH for 5 min at room temperature.
  • microtiter plates were sealed and incubated for 45 min at 37° C. After the solution was removed from wells, the plates were washed five times with 2 ⁇ SSC washing solution(0.3M sodiumchloride, 0.03M tri-sodiumcitrate), 100 ⁇ l of alkaline phosphatase-conjugated streptavidin (Gibco BRL) solution, diluted to ⁇ fraction (1/1000) ⁇ in TTBS enzyme diluting solution (0.2M Tris-HCl (pH7.6), 0.5M sodium chloride, 0.5% Tween 20), was added to each well.
  • 2 ⁇ SSC washing solution 0.03M tri-sodiumcitrate
  • TTBS enzyme diluting solution 0.2M Tris-HCl (pH7.6), 0.5M sodium chloride, 0.5% Tween 20
  • Leukocytes (Samples 5-8) which were isolated from peripheral blood (about 10 ml) of normal subjects according to usual methods, were lysed in 500 ⁇ l of guanidine thiocyanate buffer (4M guanidine thiocyanate, 25 mM sodium citrate(pH7.0), 0.5% sodium N-lauroylsarcosinate, 1% mercaptoethanol). The solution was extracted twice with phenol to eliminate proteins. After mixing with 3M sodium acetate buffer (pH 5.2, genome DNAs were obtained by adding twice volume of chilled ethanol. By using this DNAs, typing of the HLA-B40 alleles was performed as follows.
  • BASF-1 and 5′-biotinylated BASR-1 for a primer pair, amplification of the region containing the exon 2, the intron 2 and the exon 3 of the HLA-B40 alleles from DNAs described above was performed by the PCR method.
  • the reaction solution was composed of genomic DNAs (100 ng), 1.4 units of thermostable DNA which was pretreated with Taq StartTMAntibody for 5 min at room temperature, 33.5 mM Tris-HCl (pH 8.8), 8.8 mM ammonium sulfate, 1.5 mM magnesium chloride, 0.005% Tween 20, 200 ⁇ M dNTPs, and each 1.7 ⁇ M of a primer pair in a final volume of 70 ⁇ l.
  • DNA amplification was performed by using GeneAmp PCR system 9600 (Perkin Elmer) by initial denaturation at 95° C. for 2 min followed by 5 cycles of denaturation for 25 s, annealing at 70° C. for 45 s, extension at 72° C. for 45 s followed by 36 cycles of denaturation for 25 s, annealing at 65° C. for 50 s, extension at 72° C. for 45 s.
  • 5′-amino-modified DNA probes BL4, BL5, BL24, BL25, BL34, BL35, BL37, BL39, BL41, BL50, BL56, BL57, BL222A, BL409T and BL512T, were immobilized covalently on wells of carboxylate-modified polystyrene microtiter plates as follows. Twenty-five ⁇ l of the DNA probes described above which were dissolved with sterile distilled water, was added to each of 15 wells which were used for a sample, in order shown in FIG. 2 . Next, 75 ⁇ l of 0.2M EDC was added to each well and mixed.
  • GMC buffer (0.25M di-sodium hydrogenphosphate, 7% SDS, 1% BSA, 0.5M EDTA, 0.03M phosphoric acid, 20% formamide) was added to each well of the microtiter plates and the plates were incubated for 5 min at 37° C. After incubation, the buffer was removed from each well. During incubation, 60 ⁇ l of the amplified products described above, were denatured with an equivalent volume of 0.4 NaOH for 5 min at room temperature. After denaturation, 1500 ⁇ l of hybridization buffer was added to the denatured product, mixed and 100 ⁇ l of them was added to each well. The microtiter plates were sealed and incubated for 1 hour at 37° C.
  • the plates were washed five times with 2 ⁇ SSC washing solution (0.3M sodium chloride, 0.03M tri-sodium citrate), 100 ⁇ l of peroxidase-conjugated streptavidin (Vector Laboratories) solution, diluted to ⁇ fraction (1/2000) ⁇ in TTBS enzyme diluting solution (0.2M Tris-HCl (pH7.6), 0.5M sodium chloride, 0.5% Tween 20), was added to each well. The microtiter plates were sealed and incubated for 15 min at 37° C.
  • Leukocytes (Samples 9-12) which were isolated from peripheral blood (about 10 ml) of normal subjects according to usual methods, were lysed in 500 ⁇ l of guanidine thiocyanate buffer(4M guanidine thiocyanate, 25 mM sodium citrate(pH7.0), 0.5% sodium N-lauroylsarcosinate, 1% mercaptoethanol). The solution was extracted twice with phenol to eliminate proteins. After mixing with 3 M sodium acetate buffer (pH5.2), genome DNAs were obtained by adding twice volume of chilled ethanol. By using this DNAs, typing of the HLA-A antigens and alleles was performed as follows.
  • the reaction solution was composed of genomic DNAs (100 ng), 1.4 units of thermostable DNA polymerase which was pretreated with Taq StartTMAntibody for 5 min at room temperature, 33.5 mM Tris-HCl (pH 8.8), 8.8 mM ammonium sulfate, 1.5 mM magnesium chloride, 0.005% Tween 20, 200 ⁇ M dNTPs, and each 1.7 ⁇ M of a primer pair (the ratio of CGA011 to CGA012 is 4 to 1) in a final volume of 100 ⁇ l.
  • DNA amplification was performed by using GeneAmp PCR system 9600 (Perkin Elmer) by initial denaturation at 95° C.
  • 5′-amino-modified DNA probes A34, A239A, A238A, A257TC, A259AC, A282C, A282CT, A290TR, A299T, A302GR, A355G, A414A, A448C, A468T, A489A, A502C, A526T, A538CG, A538TG, A539A, A539T, A555T, A570CG and A570GT, were immobilized covalently on wells of carboxylate-modified polystyrene microtiter plates as follows.
  • GMC buffer (0.25M di-sodium hydrogenphosphate, 7% SDS, 1% BSA, 0.5M EDTA, 0.03M phosphoric acid, 20% formamide) was added to each well of the microtiter plates and the plates were incubated at 37° C. for 5 min. After incubation, the buffer of each well was removed from each well. During incubation, 96 ⁇ l of the amplified products described above, were denatured with an equivalent volume of 0.4 NaOH for 5 min at room temperature. After denaturation, 2400 ⁇ l of hybridization buffer was added to the denatured products, mixed and 100 ⁇ g of them was added to each well. The microtiter plates were sealed and incubated for 1 hour at 37° C.
  • HLA-A antigen and allele typing for each sample (9-12) was performed according to the Typing Table shown in FIG. 3 .
  • the typing results are shown in the bottom column of Table 3 as follows.
  • Leukocytes (Samples 13-16) which were isolated from peripheral blood (about 10 ml) of normal subjects according to usual methods, were lysed in 500 ⁇ l of guanidine thiocyanate buffer (4M guanidine thiocyanate, 25 mM sodium citrate(pH7.0), 0.5% sodium N-lauroylsarcosinate, 1% mercaptoethanol). The solution was extracted twice with phenol to eliminate proteins. After mixing with 3 M sodium acetate buffer (pH5.2), genome DNAs were obtained by adding twice volume of chilled ethanol. By using the DNAs, typing of the HLA-B antigen and allele was performed as follows.
  • the reaction solution was composed of genomic DNAs (100 ng), 1.4 units of thermostable DNA polymerase which was pretreated with Taq StartTMAntibody for 5 min at room temperature, 67 mM Tris-HCl (pH 8.8), 16.6 mM ammonium sulfate, 1.5 mM magnesium chloride, 0.01% Tween 20, 10% DMSO, 200 ⁇ M dNTPs, and each 1.7 ⁇ M of a primer pair (the ratio of 5BIN1-TA to 5BIN-CG is 2 to 3) in a final volume of 100 ⁇ l.
  • DNA amplification was performed by using GeneAmp PCR system 9600 (Perkin Elmer) by initial denaturation at 95° C.
  • 5′-amino-modified DNA probes BL1, BL3, BL4, BL9, BL10, BL11, BL34, BL36, BL37, BL38, BL39R, BL40, BL41, BL42, BL77, BL78, BL79, BL226G, BL263T, BL272A, BL527A, BL538CG, BL538G and BL570GT, were immobilized covalently on wells of carboxylate-modified polystyrene microtiter plates as follows.
  • GMC buffer (0.25M di-sodium hydrogenphosphate, 7% SDS, 1% BSA, 0.5M EDTA, 0.03M phosphoric acid, 20% formamide) was added to each well of the microtiter plates and the plates were incubated for 5 min at 37° C. After incubation, the buffer was removed from each well. During incubation, 96 ⁇ l of the amplified products described above, were denatured with an equivalent volume of 0.4 NaOH for 5 min at room temperature. After denaturation, 2400 ⁇ l of hybridization buffer was added to the denatured products, mixed and 100 ⁇ l of them was added to each well. The microtiter plates were sealed and incubated for 1 hour at 37° C.
  • Leukocytes (Samples 17-20) which were isolated from peripheral blood (about 10 ml) of normal subjects according to usual methods, were lysed in 500 ⁇ l of guanidine thiocyanate buffer (4M guanidine thiocyanate, 25 mM sodium citrate(pH7.0), 0.5% sodium N-lauroylsarcosinate, 1% mercaptoethanol). The solution was extracted twice with phenol to eliminate proteins. After mixing with 3M sodium acetate buffer (pH5.2), genome DNAs were obtained by adding twice volume of chilled ethanol. By using the DNAs, typing of the HLA-C alleles was performed as follows.
  • 5BCIn37-24C 5BCIn-37-24g and 5′-biotinylated 5BCIn37-34g2 for a primer pair
  • amplification of the region containing the exon 2, the intron 2 and the exon 3 of the HLA-C alleles from DNAs described above was performed by the PCR method.
  • the reaction solution was composed of genomic DNAs (100 ng), 1.4 units of thermostable DNA polymerase which was pretreated with Taq StartTMAntibody for 5 min at room temperature, 33.5 mM Tris-HCl (pH 8.8), 8.8 mM ammonium sulfate, 1.5 mM magnesium chloride, 0.005% Tween 20, 200 ⁇ M dNTPs, and each 1.7 ⁇ M of a primer pair in a final volume of 100 ⁇ l.
  • DNA amplification was performed by using GeneAmp PCR system 9600 (Perkin Elmer) by initial denaturation at 95° C. for 2 min followed by 5 cycles of denaturation for 25 s, annealing at 70° C. for 45 s, extension at 72° C. for 45 s followed by 36 cycles of denaturation for 25 s, annealing at 65° C. for 50 s, extension at 72° C. for 45 s.
  • 5′-amino-modified DNA probes 201g1, C206gR, A-12, RA-2, A-3, RA-41, A-54, B-1, RB-28, C-12, C-24, C-33, C-43, 134-g, 134-A2, 353TCA1, R341A, 343A.
  • R343g3, 353TCC, 361T1, 361T368g, 361T368T1, 369C, 387g1, 526AC2 and 538gAC were immobilized covalently on wells of carboxylate-modified polystyrene microtiter plates as follows.
  • GMC buffer (0.25M di-sodium hydrogenphosphate, 7% SDS, 1% BSA, 0.5M EDTA, 0.03M phosphoric acid, 20% formamide) was added to each well of the microtiter plates and the plates were incubated for 5 min at 37° C. After incubation, the buffer was removed from each well. During incubation, 96 ⁇ l of the amplified products described above, were denatured with an equivalent volume of 0.4 NaOH for 5 min at room temperature. After denaturation, 2400 ⁇ l of hybridization buffer solution was added to the denatured products, mixed and 100 ⁇ l of them was added to each well. The microtiter plates were sealed and incubated for 1 hour at 37° C.
  • a single HLA class I antigen or allele is determined by combining PCR amplification using a primer pair which can amplify all the HLA-A alleles, all the HLA-B alleles or all the HLA-C alleles or which is specific to the common sequence to alleles of the specific group consisting of the specific HLA-A alleles or the specific HLA-B alleles, with reverse hybridization analysis using DNA probes to enable to specifically hybridize with the sequence of al least a specific HLA-A allele, at least a specific HLA-B allele or at least a specific HLA-C allele, which are covalently immobilized on wells of microtiter plates.
  • this invention enables us to easily mechanize and automate detection and determination of the HLA class I alleles.
  • This invention offers a method, a reagent and a kit for typing of the HLA class I alleles, which are useful for judgement of compatibility between a donor and a recipient in organ transplantation and for association analysis between the HLA class I genes and various kinds of diseases in the clinical and medical field.

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JP4518784B2 (ja) * 2003-12-01 2010-08-04 Ｇ＆Ｇサイエンス株式会社 新規遺伝子型判定方法
AU2007313472B2 (en) * 2006-02-27 2014-01-16 Genomics Usa Population scale HLA-typing and uses thereof
US20090280983A1 (en) * 2008-05-08 2009-11-12 Rui Luiz Correa Picanco Fertilizer - pesticide throw-pack
WO2012047985A1 (fr) * 2010-10-06 2012-04-12 St. Jude Children's Research Hospital Typage en fonction de déterminant moléculaire d'allèles de kir et de ligands de kir
JP6160104B2 (ja) * 2013-02-08 2017-07-12 凸版印刷株式会社 Ｈｌａ−ａ＊０２グループの判定方法

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US20120157347A1 (en) * 2003-11-27 2012-06-21 Commissariat A L'energie Atomique Method for hla typing
US8435740B2 (en) * 2003-11-27 2013-05-07 Commissariat A L'energie Atomique Et Aux Energies Alternatives Method for HLA typing
EP1951894A1 (fr) * 2005-11-15 2008-08-06 CapitalBio Corporation Microreseaux pour genotypage et procedes d'utilisation
EP1951894A4 (fr) * 2005-11-15 2009-04-08 Capitalbio Corp Microreseaux pour genotypage et procedes d'utilisation
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